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It is night time in Johto. At Prof. Oak's second science lab in Cherrygrove, the special telephone receiver that Bill invented for the Mobile Pokémon Transfer System continues to receive the newest captures of Crys. With his working desk filled with all kinds of Kurt's special Pokéballs and his lab infested with the twelve Staryus that the girl caught earlier, Oak struggles to stay awake as Crys goes on talking fervently about her recent Pokémon encounters. Crys proceeds to send over a Shuckle, Magby, and Phanphy in a row, but the professor has already fallen asleep over his chair. Behind him, on the multitude of shelves where he lines up the caught Pokémon according to their dex number, there doesn't seem to have too many holes left for Crys to fill.

The next morning, Crys and Megapon are wandering through the Union Cave in hopes of finding some rare Pokémon to capture. Something lands on Megapon's head, and the little leaf Pokémon quickly freaks out. Crys picks it up into her arms, and tells it not to worry as it is only a drop of water from the cave ceiling. Crys remarks that ever since new roads have been constructed above ground, people seldom travel between Violet and Azalea via the cave anymore. She recalls Bill's mentioning about how Kanto and Johto Pokémon show variations in their appearance even if they belong to the same specie, and knows she still has lots of capturing to do for the professor.

Crys checks on the map in her Pokégear, and wishes she could find a quick way to travel to the western part of Johto where she'll meet more Pokémon she hasn't caught. Just then, a floating light appears at the far end of the cave, and Crys immediately draws back in horror with Megapon, thinking that it is some kind of lost spirit. But she soon discovers that it is just a Magneton, and wonders why such Pokémon should appear there. She decides to capture it and reaches for her Pokéballs, but little does she know that two more Magnetons have secretly crept up behind her, and together with the first Magneton she saw, unleash a strong electric field to knock her unconscious. The three magnet Pokémon then generate an electric pod to lift up the girl as well as the fainted Chicorita, and carry them over to a submarine parked along the shore of a small lake in the cave.

A while later, Lt. Surge returns from his investigations in the Union Cave, and checks on the trap he set on the ground. It turns out that the Vermillion gymleader has left the Magnetons there to guard his submarine, and devised a special trap that would capture any intruding Pokémon. Seeing that the superball he placed is empty, Lt. Surge decides that no one has been trespassing the area and quickly climbs into his submarine. Without noticing the unconscious girl at the backseat, he closes the protective shield and starts going underwater. He then accesses the vessel's communication system, and calls for a response from S.S. Aqua. A sailor returns the message that the liner is currently stationed at the southern bay of Azalea, and Lt. Surge informs him that he will arrive there soon via the secret underwater route.

After sailing through some winding passages in the water, the submarine arrives at open sea where S.S. Auqa is, and Lt. Surge prepares to enter the docking hutch under the liner. To his shock, the vessel suddenly screeches to a halt, and he looks out of the glass shield to find his submarine plagued by a whole school of Corsolas. Just then, Crys awakes at the backseat and lets out a cry when she finds herself no longer inside the Union Cave. Her sudden appearance freaks Lt. Surge out as well, and he tells her to stop fussing around.

Looking at the Corsolas belows, Lt .Surge remarks that the coral Pokémon are weighing down the submarine with their strong adhesive strength on one another. He recalls hearing about a southern sea nation where people live in communities built on Corsolas, and knows it will be difficult to break free of their constraints. He points out that they might be able to disintegrate the group by taking out their leader, but there doesn't seem to be anything they can do underwater.

Crys suddenly gets the idea of capturing the Corsola leader, and tells Lt. Surge to follow her directions. She observes the water currents intently for a brief moment, and all of a sudden urges Lt. Surge to steer towards the right as quick as he can. To the Vermillion gymleader's surprise, the submarine starts to move upwards. Turning around to see Crys's Natu, he wonders if it is lifting their vessel up with its psychic powers, but Crys explains that it is the water current that's carrying them up, and Lt. Surge is secretly impressed by the girl's awareness of the things around her. Once the submarine surfaces above water, Crys quickly slides open the glass shield and locates the leader of the Corsolas. She immediately has Naton deliver a psychic attack to stun it, and proceeds to kick off a lureball, instantly capturing it. The whole school of Corsolas then disintegrates and falls back into the sea while Lt. Surge remains speechless at what he just witnessed.

Later, on S.S. Aqua, the sailor tells Crys that she is on the new luxurious liner that circulates between Kanto and Johto. He remarks that the ship departs from the Olivine seaport every Monday, Wednesday and Friday, and says they are currently on their way back there to let new passengers get on. Looking around around the giant liner, Crys wonders if it belongs to Lt. Surge, but the sailor seems hesitant in his answer. He pulls Crys aside, and whispers that he has actually heard rumours about the Vermillion gymleader using another luxurious liner in Kanto called S.S. Anne for criminal purposes in the past. Just then, Lt .Surge appears on the dock, and the sailor quickly shuts his mouth. Lt. Surge tells Crys that they are approaching the west of Johto where she wanted to go, and gives her a friendly slap on the back, thanking her for helping him out earlier.

A few moments later, as Crys steps onto the Olivine seaport to continue on her journey, Lt. Surge sends the sailor off to do some work, and starts pondering on his own upcoming plan…